{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T13:27:58Z","timestamp":1786368478641,"version":"build-2736575974"},"reference-count":71,"publisher":"American Chemical Society (ACS)","issue":"15","license":[{"start":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T00:00:00Z","timestamp":1781136000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T00:00:00Z","timestamp":1781136000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T00:00:00Z","timestamp":1781136000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2024YFC3607500"],"award-info":[{"award-number":["2024YFC3607500"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017700","name":"Henan Provincial Science and Technology Research Project","doi-asserted-by":"publisher","award":["262102310410"],"award-info":[{"award-number":["262102310410"]}],"id":[{"id":"10.13039\/501100017700","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research","award":["FKLDSR-202501"],"award-info":[{"award-number":["FKLDSR-202501"]}]},{"name":"GHfund","award":["202407016681"],"award-info":[{"award-number":["202407016681"]}]},{"name":"Key Research and Development Project in Henan Province","award":["241111114200"],"award-info":[{"award-number":["241111114200"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Lysine-specific demethylase 1 (LSD1\/KDM1A) is a key epigenetic regulator that modulates chromatin dynamics and transcriptional programs through both catalytic demethylation and scaffold-mediated interactions, rendering it an attractive therapeutic target. Although numerous reversible LSD1 inhibitors have been developed, their structural diversity and binding complexity remain insufficiently characterized due to limited structural data. Here, we combined cheminformatics with cutting-edge cofolding\u2013based structural prediction to systematically map the chemical and conformational landscape of reversible LSD1 inhibitors. Our analysis delineated distinct chemical clusters with uneven scaffold distributions, revealing substantial, computationally unexplored regions within the current inhibitor repertoire whose druggability awaits experimental confirmation. Consistent predictions across three state-of-the-art cofolding models uncovered several novel scaffolds with nanomolar potency and previously unrecognized binding modes. In our data set, intermodel prediction consistency was positively associated with both structurally similarity to training data ligands and experimental inhibitory activity. Notably, AlphaFold3 achieved superior accuracy under sparse-data conditions. Besides, cofolding models effectively captured ligand-induced conformational changes (induced-fit effect) but failed to account for allosteric regulation. Together, these findings establish a high-resolution structural atlas of reversible LSD1 inhibitors and provide practical guidance for rational scaffold optimization. Beyond LSD1, this work offers methodological insights into leveraging cofolding\u2013driven prediction for structure-based drug design.<\/jats:p>","DOI":"10.1021\/acs.jcim.5c03188","type":"journal-article","created":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T03:43:49Z","timestamp":1781235829000},"page":"9262-9276","source":"Crossref","is-referenced-by-count":0,"title":["Co-Folding\u2013Driven\nStructural Mapping of Reversible\nLSD1 Inhibitors Reveals Unexplored Chemical Space and Binding Diversity"],"prefix":"10.1021","volume":"66","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9664-1395","authenticated-orcid":true,"given":"Kecheng","family":"Yang","sequence":"first","affiliation":[{"name":"Zhengzhou University , , ,","place":["Zhengzhou, China, 450001"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wentao","family":"Yang","sequence":"additional","affiliation":[{"name":"Zhengzhou University , , ,","place":["Zhengzhou, China, 450001"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Longwei","family":"Guo","sequence":"additional","affiliation":[{"name":"Zhengzhou University , , ,","place":["Zhengzhou, China, 450001"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinyu","family":"Wang","sequence":"additional","affiliation":[{"name":"Zhengzhou University , , ,","place":["Zhengzhou, China, 450001"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongmin","family":"Liu","sequence":"additional","affiliation":[{"name":"Zhengzhou University , , ,","place":["Zhengzhou, China, 450001"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoquan","family":"Feng","sequence":"additional","affiliation":[{"name":"Zhengzhou University , , ,","place":["Zhengzhou, China, 450001"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7827-5678","authenticated-orcid":true,"given":"Yuefeng","family":"Bi","sequence":"additional","affiliation":[{"name":"Zhengzhou University , , ,","place":["Zhengzhou, China, 450001"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaole","family":"Chen","sequence":"additional","affiliation":[{"name":"Fujian Medical University , , ,","place":["Fuzhou, China, 350004"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xu","family":"Gao","sequence":"additional","affiliation":[{"name":"Zhengzhou University , , ,","place":["Zhengzhou, China, 450001"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,6,11]]},"reference":[{"issue":"1","key":"2026081008094445300_cit1","doi-asserted-by":"publisher","first-page":"340","DOI":"10.1038\/s41392-024-02030-9","article-title":"Chromatin\naccessibility: biological functions, molecular\nmechanisms and therapeutic application","volume":"9","author":"Chen","year":"2024","journal-title":"Signal\nTransduction Targeted Ther."},{"issue":"4","key":"2026081008094445300_cit2","doi-asserted-by":"publisher","DOI":"10.1038\/emm.2017.11","article-title":"Writing, erasing and\nreading histone lysine methylations","volume":"49","author":"Hyun","year":"2017","journal-title":"Exp. Mol.\nMed."},{"issue":"7","key":"2026081008094445300_cit3","doi-asserted-by":"publisher","first-page":"941","DOI":"10.1016\/j.cell.2004.12.012","article-title":"Histone demethylation\nmediated by the nuclear amine oxidase homolog LSD1","volume":"119","author":"Shi","year":"2004","journal-title":"Cell"},{"key":"2026081008094445300_cit4","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1038\/nature04020","article-title":"LSD1 demethylates\nrepressive histone\nmarks to promote androgen-receptor-dependent transcription","volume":"437","author":"Metzger","year":"2005","journal-title":"Nature"},{"issue":"12","key":"2026081008094445300_cit5","doi-asserted-by":"publisher","first-page":"1936","DOI":"10.1038\/s12276-020-00542-2","article-title":"LSD1: more\nthan demethylation of histone lysine residues","volume":"52","author":"Perillo","year":"2020","journal-title":"Exp. Mol. Med."},{"issue":"1","key":"2026081008094445300_cit6","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1016\/j.molcel.2010.06.006","article-title":"Lysine methylation regulates E2F1-induced\ncell death","volume":"39","author":"Kontaki","year":"2010","journal-title":"Mol. Cell"},{"issue":"3","key":"2026081008094445300_cit7","doi-asserted-by":"publisher","first-page":"129","DOI":"10.4161\/epi.4.3.8443","article-title":"LSD1 demethylates histone\nand non-histone proteins","volume":"4","author":"Nicholson","year":"2009","journal-title":"Epigenetics"},{"issue":"39","key":"2026081008094445300_cit8","doi-asserted-by":"publisher","first-page":"5512","DOI":"10.1038\/onc.2017.158","article-title":"LSD1 demethylates HIF1\u03b1\nto inhibit hydroxylation\nand ubiquitin-mediated degradation in tumor angiogenesis","volume":"36","author":"Lee","year":"2017","journal-title":"Oncogene"},{"issue":"1","key":"2026081008094445300_cit9","doi-asserted-by":"publisher","first-page":"105737","DOI":"10.1016\/j.isci.2022.105737","article-title":"The scaffolding function of LSD1\/KDM1A reinforces a\nnegative feedback loop to repress stem cell gene expression during\nprimitive hematopoiesis","volume":"26","author":"Casey","year":"2023","journal-title":"iScience"},{"issue":"25","key":"2026081008094445300_cit10","doi-asserted-by":"publisher","first-page":"12311","DOI":"10.1073\/pnas.1902012116","article-title":"LSD1 destabilizes FBXW7 and abrogates\nFBXW7 functions independent of its demethylase activity","volume":"116","author":"Lan","year":"2019","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"issue":"18","key":"2026081008094445300_cit11","doi-asserted-by":"publisher","first-page":"E4179","DOI":"10.1073\/pnas.1719168115","article-title":"LSD1\nactivates a lethal prostate cancer gene network independently\nof its demethylase function","volume":"115","author":"Sehrawat","year":"2018","journal-title":"Proc. Natl. Acad.\nSci. U. S. A."},{"key":"2026081008094445300_cit12","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1016\/j.tips.2025.01.006","article-title":"Leveraging non-enzymatic functions of LSD1 for novel therapeutics","volume":"46","author":"Song","year":"2025","journal-title":"Trends Pharmacol. Sci."},{"issue":"1","key":"2026081008094445300_cit13","doi-asserted-by":"publisher","first-page":"7758","DOI":"10.1038\/s41467-024-51966-7","article-title":"The scaffolding\nfunction of LSD1 controls DNA methylation in mouse ESCs","volume":"15","author":"Malla","year":"2024","journal-title":"Nat. Commun."},{"issue":"7","key":"2026081008094445300_cit14","doi-asserted-by":"publisher","first-page":"1747","DOI":"10.1016\/j.cell.2025.02.023","article-title":"20 years\nof histone lysine demethylases: From discovery to the clinic and beyond","volume":"188","author":"Gray","year":"2025","journal-title":"Cell"},{"issue":"1","key":"2026081008094445300_cit15","doi-asserted-by":"publisher","first-page":"4327","DOI":"10.1038\/s41467-024-48607-4","article-title":"Priming with LSD1 inhibitors promotes\nthe persistence and antitumor effect of adoptively transferred T cells","volume":"15","author":"Qiu","year":"2024","journal-title":"Nat. Commun."},{"issue":"11","key":"2026081008094445300_cit16","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aba1187","article-title":"LSD1 enzyme\ninhibitor TAK-418 unlocks aberrant epigenetic\nmachinery and improves autism symptoms in neurodevelopmental disorder\nmodels","volume":"7","author":"Baba","year":"2021","journal-title":"Sci. Adv."},{"issue":"4","key":"2026081008094445300_cit17","doi-asserted-by":"publisher","first-page":"797","DOI":"10.1007\/s12026-024-09486-5","article-title":"Inhibition of LSD1\nvia SP2509 attenuated\nthe progression of rheumatoid arthritis","volume":"72","author":"Yu","year":"2024","journal-title":"Immunol.\nRes."},{"issue":"8","key":"2026081008094445300_cit18","doi-asserted-by":"publisher","first-page":"1122","DOI":"10.1016\/j.scib.2024.01.015","article-title":"LSD1 promotes\nthe FSH responsive follicle formation by regulating\nautophagy and repressing Wt1 in the granulosa cells","volume":"69","author":"Zhu","year":"2024","journal-title":"Sci. Bull."},{"key":"2026081008094445300_cit19","doi-asserted-by":"publisher","first-page":"101430","DOI":"10.1016\/j.jpha.2025.101430","article-title":"Comparative analysis for optimal LSD1 inhibitors evaluation techniques:pros\nand cons","volume":"16","author":"Yin","year":"2026","journal-title":"J. Pharm. Anal."},{"key":"2026081008094445300_cit20","doi-asserted-by":"publisher","first-page":"217093","DOI":"10.1016\/j.canlet.2024.217093","article-title":"Targeting LSD1 in cancer: Molecular\nelucidation and recent advances","volume":"598","author":"Cai","year":"2024","journal-title":"Cancer Lett."},{"issue":"1","key":"2026081008094445300_cit21","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1021\/acs.jpcb.3c06900","article-title":"Uncovering New Conformational States\nof the Substrate Binding Pocket\nof LSD1 Potential for Inhibitor Design via Funnel Metadynamics","volume":"128","author":"Yang","year":"2024","journal-title":"J. Phys. Chem. B"},{"issue":"5","key":"2026081008094445300_cit22","doi-asserted-by":"publisher","first-page":"903","DOI":"10.1016\/j.molcel.2020.04.019","article-title":"Crystal Structure of\nthe LSD1\/CoREST Histone Demethylase Bound to Its Nucleosome Substrate","volume":"78","author":"Kim","year":"2020","journal-title":"Mol. 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Hematol.\nOncol."},{"key":"2026081008094445300_cit26","doi-asserted-by":"publisher","first-page":"550","DOI":"10.3390\/molecules29020550","article-title":"Lysine-Specific\nDemethylase 1 Inhibitors: A Comprehensive Review Utilizing Computer-Aided\nDrug Design Technologies","volume":"29","author":"Han","year":"2024","journal-title":"Molecules"},{"issue":"5","key":"2026081008094445300_cit27","doi-asserted-by":"publisher","first-page":"2466","DOI":"10.1021\/acs.jmedchem.0c02176","article-title":"Reversible Lysine\nSpecific Demethylase 1 (LSD1) Inhibitors:\nA Promising Wrench to Impair LSD1","volume":"64","author":"Dai","year":"2021","journal-title":"J. Med. Chem."},{"key":"2026081008094445300_cit28","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1146\/annurev-biochem-030222-120000","article-title":"The Art\nand Science of Molecular\nDocking","volume":"93","author":"Paggi","year":"2024","journal-title":"Annu. Rev. Biochem."},{"issue":"2","key":"2026081008094445300_cit29","doi-asserted-by":"publisher","first-page":"895","DOI":"10.1021\/acs.jcim.8b00545","article-title":"Comparative\nAssessment of Scoring Functions: The CASF-2016\nUpdate","volume":"59","author":"Su","year":"2019","journal-title":"J. Chem. Inf. Model."},{"issue":"11","key":"2026081008094445300_cit30","doi-asserted-by":"publisher","first-page":"12125","DOI":"10.1021\/acs.jmedchem.5c00966","article-title":"Unveiling New Binding\nSites and Allosteric\nRegulation Mechanisms of LSD1 for Novel Therapeutics","volume":"68","author":"Yang","year":"2025","journal-title":"J. Med. Chem."},{"issue":"8016","key":"2026081008094445300_cit31","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate\nstructure prediction of biomolecular\ninteractions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"2026081008094445300_cit32","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1002\/prot.70044","article-title":"AlphaFold3\nat CASP16","author":"Elofsson","year":"2025","journal-title":"bioRxiv"},{"issue":"1","key":"2026081008094445300_cit33","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic\nAcids Res."},{"issue":"D1","key":"2026081008094445300_cit34","doi-asserted-by":"publisher","first-page":"D1180","DOI":"10.1093\/nar\/gkad1004","article-title":"The ChEMBL\nDatabase\nin 2023: a drug discovery platform spanning multiple bioactivity data\ntypes and time periods","volume":"52","author":"Zdrazil","year":"2024","journal-title":"Nucleic Acids Res."},{"issue":"11","key":"2026081008094445300_cit35","doi-asserted-by":"publisher","first-page":"1486","DOI":"10.1016\/j.chembiol.2019.09.012","article-title":"Recent Advances\nin Selective and Irreversible Covalent Ligand Development and Validation","volume":"26","author":"Zhang","year":"2019","journal-title":"Cell Chem. Biol."},{"key":"2026081008094445300_cit36","unstructured":"Landrum, G.\n          \n          Rdkit documentation.\nRelease 1. 1\u201379, 2013."},{"issue":"5","key":"2026081008094445300_cit37","doi-asserted-by":"publisher","first-page":"742","DOI":"10.1021\/ci100050t","article-title":"Extended-Connectivity Fingerprints","volume":"50","author":"Rogers","year":"2010","journal-title":"J. Chem.\nInf. Model."},{"issue":"1","key":"2026081008094445300_cit38","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1186\/s13321-015-0069-3","article-title":"Why is Tanimoto index an appropriate\nchoice for fingerprint-based similarity calculations?","volume":"7","author":"Bajusz","year":"2015","journal-title":"J. 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Comput. Chem."},{"issue":"1","key":"2026081008094445300_cit52","first-page":"82","article-title":"Pymol:\nAn open-source molecular graphics tool","volume":"40","author":"DeLano","year":"2002","journal-title":"CCP4\nNewsl. Protein Crystallogr."},{"issue":"W1","key":"2026081008094445300_cit53","doi-asserted-by":"publisher","first-page":"W463","DOI":"10.1093\/nar\/gkaf361","article-title":"PLIP 2025:\nintroducing protein\u2013protein interactions to the protein\u2013ligand\ninteraction profiler","volume":"53","author":"Schake","year":"2025","journal-title":"Nucleic Acids Res."},{"issue":"3","key":"2026081008094445300_cit54","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: fundamental\nalgorithms for scientific computing in Python","volume":"17","author":"Virtanen","year":"2020","journal-title":"Nat. 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